Revision as of 10:21, 26 October 2012

The SWAT4LS Hackathon is an informal event associated with the SWAT4LS Semantic Web Applications and Tools for Life Sciences Workshops Series.

Scope of the event is to bring together experts and enthusiasts in the application of semantic technologies in healthcare and life science for open discussion and jam coding sessions.
The Hackathon will be organized on the 28th of November 2012 at La Cantine, Paris (map).

While the agenda will be open, we are coordinating ideas that can be developd at the network in advance, to maximize the utility of the day. Co-organizers for each community will help gathering ideas and finding point of contacts.

WikiPathways community

Contact Point

Andra Waagmeester

Introduction

WikiPathways is a online resource for pathways. Content is provided by the audience at large. I currently contains more then 2200 pathways from 21 species source. Pathways are captured in a XML-based format GPML. Recently WikiPathways was exposed as linked open data where GPML content was exported as RDF. This data is available through a SPARQL endpoint http://sparql.wikipathways.org.

Database Center for Life Sciences Community / BioHackathon

Contact Point

Proposed action points

W3C HCLS Community

Contact Point

Proposed action points

Making an online inventory of available resources (wiki) to document underlying schemas of available datasources.

There are nice lists of active SPARQL endpoints (example 1) and (example 2). Finding where the data actually links can still be challenging.

It would be really beneficial to create an overview with descriptions of different linked data sets describing the underlying structure. The first step would be to define a format where data providers describe their data in a predefined (wiki) format. This format could be based on VoID.
These description coulds then be used to create so called data landscapes in tools such as Semscape.

Creating a review of sparql endpoints and their support for remote federated queries.

Within a federated query you can query different flavours of sparql endpoints. SInce different endpoints have their own implementations and support for different SPARQL versions, it is essential to understand the different issues each type of endpoint might have. The community would benefit from a list mentioning each available SPARQL endpoint system (e.g. 4store, virtuoso, etc) and their support for different SPARQL versions. Also this list could mention specific features (e.g. soft limit in 4store) influencing the recall in federated queries.

BioPAX Community

Contact Point

Ismael Navas Delgado

Proposed action points

Confirmed Participants

Ismael Navas Delgado

Andrea Splendiani

Resources

PathwayCommons SPARQL endpoint. Endpoint over all BioPAX representations in PathwayCommons